Open Data supplied by Natural Environment Research Council (NERC)

Neil Brown MK3 CTD

The Neil Brown MK3 conductivity-temperature-depth (CTD) profiler consists of an integral unit containing pressure, temperature and conductivity sensors with an optional dissolved oxygen sensor in a pressure-hardened casing. The most widely used variant in the 1980s and 1990s was the MK3B. An upgrade to this, the MK3C, was developed to meet the requirements of the WOCE project.

The MK3C includes a low hysteresis, titanium strain gauge pressure transducer. The transducer temperature is measured separately, allowing correction for the effects of temperature on pressure measurements. The MK3C conductivity cell features a free flow, internal field design that eliminates ducted pumping and is not affected by external metallic objects such as guard cages and external sensors.

Additional optional sensors include pH and a pressure-temperature fluorometer. The instrument is no longer in production, but is supported (repair and calibration) by General Oceanics.

Aquatracka fluorometer

The Chelsea Instruments Aquatracka is a logarithmic response fluorometer. It uses a pulsed (5.5 Hz) xenon light source discharging between 320 and 800 nm through a blue filter with a peak transmission of 420 nm and a bandwidth at half maximum of 100 nm. A red filter with sharp cut off, 10% transmission at 664 nm and 678 nm, is used to pass chlorophyll-a fluorescence to the sample photodiode.

The instrument may be deployed either in a through-flow tank, on a CTD frame or moored with a data logging package.

This sensor was originally designed to assist the study of marine photosynthesis. With the use of logarithmic amplication, the sensor covers a range of 6 orders of magnitude, which avoids setting up the sensor range for the expected signal level for different ambient conditions.

The sensor consists of a hollow PTFE 2-pi collector supported by a clear acetal dome diverting light to a filter and photodiode from which a cosine response is obtained. The sensor can be used in moorings, profiling or deployed in towed vehicles and can measure both upwelling and downwelling light.

SeaTech Transmissometer

Introduction

The transmissometer is designed to accurately measure the the amount of light transmitted by a modulated Light Emitting Diode (LED) through a fixed-length in-situ water column to a synchronous detector.

Specifications

Water path length: 5 cm (for use in turbid waters) to 1 m (for use in clear ocean waters).

Notes

The instrument can be interfaced to Aanderaa RCM7 current meters. This is achieved by fitting the transmissometer in a slot cut into a customized RCM4-type vane.

A red LED (660 nm) is used for general applications looking at water column sediment load. However, green or blue LEDs can be fitted for specilised optics applications. The light source used is identified by the BODC parameter code.

Components of the CTD data set

Data Acquisition and On-Board Processing

Instrumentation

The CTD profiles were taken with an RVS Neil Brown Mk3B CTD incorporating a pressure sensor, conductivity cell, platinum resistance thermometer and a Beckmann dissolved oxygen sensor (fed by a SeaBird pump). The CTD unit was mounted vertically in the centre of a protective cage approximately 1.5m square. Attached to the bars of the frame were a Chelsea Instruments Aquatracka fluorometer and a SeaTech red light (661 nm) transmissometer with a 25cm path length.

Above the frame was a General Oceanics rosette sampler fitted with twelve 10-litre water bottles. These comprised a mixture of Niskin and ultra-clean teflon lined Go-Flo bottles as dictated by sampling requirements. The bases of the bottles were 0.75 metres above the pressure head and their tops 1.55 metres above it. One bottle was fitted with a holder for twin digital reversing thermometers mounted 1.38 metres above the CTD temperature sensor.

Above the rosette was a PML 2pi PAR (photosynthetically available scalar radiation) sensor pointing upwards to measure downwelling irradiance. A second 2pi PAR sensor, pointing downwards, was fitted to the bottom of the cage to measure upwelling irradiance. It should be noted that these sensors were vertically separated by 2 metres with the upwelling sensor 0.2 metres below the pressure head and the downwelling sensor 1.75 metres above it.

No account has been taken of rig geometry in the compilation of the CTD data set. However, all water bottle sampling depths have been corrected for rig geometry and represent the true position of the midpoint of the water bottle in the water column.

Data Acquisition

On each cast, the CTD was lowered continuously at 0.5 to 1.0 m s-1 to the closest comfortable proximity to the sea floor. The upcast was done in stages between the bottle firing depths.

Data were logged by the RVS ABC data logging system. Output channels from the deck unit were logged at 32 Hz by a microprocessor interface (the Level A) which passed time-stamped averaged cycles at 1 Hz to a Sun workstation (the Level C) via a buffering system (the Level B).

On-Board Data Processing

The raw data comprised ADC counts. These were converted into engineering units (volts for PAR meters, fluorometer and transmissometer; ml l-1 for oxygen; mmho cm-1 for conductivity; 7 °C for temperature; decibars for pressure) by the application of laboratory determined calibrations. Salinity (Practical Salinity Units as defined in Fofonoff and Millard, 1983) was calculated from the conductivity ratios (conductivity/42.914) and a time lagged temperature using the function described in UNESCO Report 37 (1981).

The data set was submitted to BODC in this form on Quarter Inch Cartridge tapes in RVS internal format for post-cruise processing and data banking.

Post-Cruise Processing and Calibration at BODC

Reformatting

The data were converted into the BODC internal format to allow the use of in-house software tools, notably the workstation graphics editor. In addition to reformatting, the transfer program applied the following modifications to the data:

Dissolved oxygen was corrected using a modified algorithm to allow for the pumped water supply and arbitrary calibration coefficients. The resultant data were in arbitrary units, linearly proportional to the true value, which could be screened and held, pending delivery of the true calibration coefficients.

Transmissometer voltages were corrected to the manufacturer's specified voltage by ratio using transmissometer air readings taken during the cruise.

Transmissometer voltages were converted to percentage transmission by multiplying them by a factor of 20.

The transmissometer data were converted to attenuance using the algorithm:-

Attenuance (m-1) = -4 loge (% transmission/100)

Editing

Reformatted CTD data were transferred onto a high-speed graphics workstation. Using custom in-house graphics editors, downcasts and upcasts were differentiated and the limits of the downcasts and upcasts were manually flagged.

Spikes on all the downcast channels were manually flagged. No data values were edited or deleted; flagging was achieved by modification of the associated quality control flag.

The pressure ranges over which the bottle samples had been collected were logged by manual interaction with the software. Usually, the marked reaction of the oxygen sensor to the bottle firing sequence was used to determine this. These pressure ranges were subsequently used, in conjunction with a geometrical correction for the position of the water bottles with respect to the CTD pressure transducer, to determine the pressure range of data to be averaged for calibration values.

Once screened on the workstation, the CTD downcasts were loaded into a database under the ORACLE Relational Database Management System.

For this cruise, the RVS Neil Brown Mk 3B CTD system was equipped with a SeaBird pump, which sent water at a constant rate through the housing containing the existing Beckman oxygen electrode. Problems associated with the plumbing of the pump to the oxygen probe resulted in many profiles only recording good oxygen data on upcasts. To overcome this, the upcast data for oxygen, temperature and salinity channels were flagged to remove any spikes. The downcast oxygen values loaded into ORACLE were then replaced where necessary by upcast oxygen data using isopycnal (rather than pressure) matching to determine the replacement values to be used.

Calibration

With the exception of pressure, calibrations were done by comparison of CTD data against measurements made on water bottle samples or from the reversing thermometers mounted on the water bottles as in the case of temperature. In general, values were averaged from the CTD downcasts but where visual inspection of the data showed significant hysteresis values were manually extracted from the CTD upcasts.

All calibrations described here have been applied to the data.

Pressure

The pressure offset was determined by looking at the pressures recorded when the CTD was clearly logging in air (readily apparent from the conductivity channel). The following correction (consistent throughout both legs of CD93 within ±0.05 dbar) was applied:

Pcorr = P - 0.43 (standard deviation = 0.05)

Temperature

The CTD temperature was compared with SIS digital reversing thermometers attached to the instrument frame. These were found to agree within 0.007 °C. No correction has been applied as the platinum resistance thermometer is believed to be at least as reliable as the reversing thermometers.

Salinity

During screening a number of offsets were noted in the salinity trace. These were attributed to the conductivity cell contamination. The following corrections have been applied:

CP 89

0.02 PSU added between 366.6 db and 446.2 db

CP 89

0.01 PSU added between 559.6 db and 566.1 db

CP 90

0.016 PSU added between 0 db and 340 db

CP 110

0.006 PSU added between 627.0 db and 632.5 db

CP 116

0.019 PSU less between 344.0 db and 349.0 db

CP 183

0.012 PSU added between 158.0 db and 182.1 db

CP 183

0.01 PSU added between 188.8 db and 192.1 db

CP 188

0.0214 PSU added between 12.0 db and 30.0 db

CP 188

0.0096 PSU added between 0 db and 625 db

Salinity was calibrated against water bottle samples measured on the Guideline 55358 AutoLab Salinometer during the cruise.

Samples were collected in glass bottles filled to just below the neck and sealed with plastic stoppers. Batches of samples were left for at least 24 hours to reach thermal equilibrium in the lab containing the salinometer before analysis.

The correction determined for this cruise was:

Scorr = S + 0.027 (standard deviation 0.006)

Upwelling and Downwelling Irradiance

The PAR voltages were converted to Wm-2 using the following equations determined in February 1990 supplied by RVS.

Upwelling (#10):

PAR (Wm-2) = exp (-5.090*volts + 6.6470)/100

Downwelling (#12):

PAR (Wm-2) = exp (-4.978*volts + 6.7770)/100

Note that these sensors have been empirically calibrated to obtain a conversion from W/m2 into µE/m2/s, which may be effected by multiplying the data given by 3.75.

Optical Attenuance and Suspended Particulate Matter

The air correction applied for this cruise was based on an air reading obtained during the cruise (4.789V). The manufacturer's voltage for the instrument used (SN115D) was 4.805V.

Large volume samples were taken for gravimetric analysis of the suspended particulate matter concentration. These were used to generate calibrations that expressed attenuance in terms of suspended particulate matter concentrations.

Robin McCandliss (University of Wales, Bangor) undertook this work, under the supervision of Sarah Jones. The optimal approach developed was to base the calibration on samples taken from near the seabed (i.e. those with the minimum content of fluorescent material). The data from all SES cruises where SPM samples were taken were pooled to derive the calibration equation:

SPM (mg/l) = (2.368*Atten) - 0.801 (R2 = 79%)

This calibration is valid for all SES cruises after and including Charles Darwin cruise CD93A. The clear water attenuance predicted by the equation is 0.336 per m, which agrees well with literature values.

No attempt has been made to replace attenuance by SPM concentration in the final data set. However, users may use the equation above to compute an estimated SPM channel from attenuance when required.

Chlorophyll

200ml of seawater collected at several depths on each cast were filtered and the papers frozen for acetone extraction and fluorometric analysis on land. 352 extracted chlorophyll concentrations (range 0.04 to 5.38 mg/m3) were regressed against the corresponding fluorometer voltages. The following relationship was found:

This calibration was based on pooled sample data from legs A and B of this cruise.

Attempts were made to derive a correction based on ambient light levels recorded by the CTD radiation sensors, but with no success for those casts where surface inhibition was most evident.

The calibration equation above was applied to the whole data set.

The surface inhibition problem was addressed by manual editing of fluorometer voltages. The fluorometer voltage readings in the top 10 metres were manually edited where both of the following criteria were satisfied:

calibrated CTD values at the surface were more than 0.8 mg/m3 lower than the corresponding extracted chlorophyll value.

the CTD fluorescence signal was not supported by the transmission signal in the top 10 metres.

The following profiles from this cruise leg have been edited to remove surface quench effects:

CP61, CP62, CP63, CP76, CP89, CP92, CP100, CP101, CP102, CP103, CP194

Dissolved Oxygen

Dissolved oxygen concentrations were determined by micro-Winkler titration of seawater samples taken from a range of depths on several CTD casts. These values were compared with oxygen readings derived from the oxygen sensor membrane current, oxygen sensor temperature, sea temperature and salinity values recorded by the CTD on the upcast. Hilary Wilson (University of Wales, Bangor) carried out this work, under the supervision of Dr. Paul Tett. The following equation was supplied to BODC and the coefficients A and B were applied to the data:

[O2] = (A*C + B )* S' ml/l

where

A =

1.760 (casts 148 and 159),

2.754 (casts 60 to 147, 149 to 158, 160 to 196)

C =

oxygen sensor current ( A)

B =

-0.309 (casts 148 and 159),

-0.0176 (casts 60 to147, 149 to158, 160 to196)

S'=

oxygen saturation concentration (a function of water temperature and salinity).

Finally, the data were converted to µM by multiplication by 44.66.

Considerable manipulation of the oxygen data, such as the substitution of downcast data by isopycnal-matched upcast data, was required to produce the oxygen data channel in the final data set. This, combined with the uncertainties involved in the calibration of oxygen data, might mean that some users would wish to re-examine the oxygen processing. To facilitate this, BODC have systematically archived the raw data (including oxygen current and temperature) from both upcasts and downcasts. These data are available on request.

Data Reduction

Once all screening and calibration procedures were completed, the data set was binned to 2 db (casts deeper than 100 db) or 1 db (casts shallower than 100 db). The binning algorithm excluded any data points flagged suspect and attempted linear interpolation over gaps up to 3 bins wide. If any gaps larger than this were encountered, the data in the gaps were set null.

Oxygen saturation has been computed using the algorithm of Benson and Krause (1984).

References

Benson B.B. and Krause D. jnr. 1984. The concentration and isotopic fractionation of oxygen dissolved in fresh water and sea water in equilibrium with the atmosphere. Limnol. Oceanogr. 29 pp.620-632.

Land Ocean Interaction Study (LOIS)

Introduction

The Land Ocean Interaction Study (LOIS) was a Community Research Project of the Natural Environment Research Council (NERC). The broad aim of LOIS was to gain an understanding of, and an ability to predict, the nature of environmental change in the coastal zone around the UK through an integrated study from the river catchments through to the shelf break.

LOIS was a collaborative, multidisciplinary study undertaken by scientists from NERC research laboratories and Higher Education institutions. The LOIS project was managed from NERC's Plymouth Marine Laboratory.

The project ran for six years from April 1992 until April 1998 with a further modelling and synthesis phase beginning in April 1998 and ending in April 2000.

Marine Fieldwork

Marine field data were collected between September 1993 and September 1997 as part of RACS(C) and SES. The RACS data were collected throughout this period from the estuaries and coastal waters of the UK North Sea coast from Great Yarmouth to the Tweed. The SES data were collected between March 1995 and September 1996 from the Hebridean slope. Both the RACS and SES data sets incorporate a broad spectrum of measurements collected using moored instruments and research vessel surveys.

LOIS Shelf Edge Study (LOIS - SES)

Introduction

SES was a component of the NERC Land Ocean Interaction Study (LOIS) Community Research Programme that made intensive measurements from the shelf break in the region known as the Hebridean Slope from March 1995 to September 1996.

Scientific Rationale

SES was devoted to the study of interactions between the shelf seas and the open ocean. The specific objectives of the project were:

To identify the time and space scales of ocean-shelf momentum transmission and to quantify the contributions to ocean-shelf water exchange by physical processes.

To estimate fluxes of water, heat and certain dissolved and suspended constituents across a section of the shelf edge with special emphasis on net carbon export from, and nutrient import to, the shelf.

To incorporate process understanding into models and test these models by comparison with observations and provide a basis for estimation of fluxes integrated over time and the length of the shelf.

Fieldwork

The SES fieldwork was focussed on a box enclosing two sections across the shelf break at 56.4-56.5 °N and 56.6-56.7 °N. Moored instrument arrays were maintained throughout the experiment at stations with water depths ranging from 140 m to 1500 m, although there were heavy losses due to the intensive fishing activity in the area. The moorings included meteorological buoys, current meters, transmissometers, fluorometers, nutrient analysers (but these never returned any usable data), thermistor chains, colour sensors and sediment traps.

The moorings were serviced by research cruises at approximately three-monthly intervals. In addition to the mooring work this cruises undertook intensive CTD, water bottle and benthic surveys with cruise durations of up to 6 weeks (3 legs of approximately 2 weeks each).

Moored instrument activities associated with SES comprised current measurements in the North Channel in 1993 and the Tiree Passage from 1995-1996. These provided boundary conditions for SES modelling activities.

Additional data were provided through cruises undertaken by the Defence Evaluation and Research Agency (DERA) in a co-operative programme known as SESAME.

Related series for this Fixed Station are presented in the table below. Further information can be found by following the appropriate links.

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